B3
12
10
3
2
B3
12
10
3
2
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
The figure for this sample couldn't be processed. The per-base N density across the sample is within the interquartile range for this sample with no outliers.Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
Figure 1. Subconsensus Variant Read Counts. The sample pileup was analyzed to find positions in the genome where the non-reference allele percentage was >=15%. All positions with >=10 reads, a positional read base quality of >=10 and a map quality >=30 were included in the analysis.
The summary table contains all of the variants called by iVar variants
with a minimum alternate allele threshold of >=60% and a
minimum read depth of 10.
This table may not exactly match the variants called in the final
consensus sequence as there is a slight difference in how
iVar variants and iVar consensus call them,
mostly surrounding indels, along with the iVar consensus
threshold being set at >=75%. The threshold difference
between the two is there to hopefully catch most of these rare indel
differences.
Figure 2. Positional genomic depth. The Y-axis is log-scaled so positions with no genomic depth have been set to 1 to allow a continuous visualization. Zones have been marked using a colour scheme where: 0-10 is red corresponding to masked sites, 10-30 is yellow corresponding to sites where there is a basecall but limited depth, and 30+ is green for positions with acceptable or better depth.
Figure 3. Average root-mean-square read base quality score per genomic position
Figure 4. The percentage of base calls at each position for which an N was called along the genome. The displayed positions are those identified as outliers by using quartile ranges.
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